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Aliases for TBC1D20 Gene

Aliases for TBC1D20 Gene

  • TBC1 Domain Family Member 20 2 3 5
  • C20orf140 3 4
  • Chromosome 20 Open Reading Frame 140 2
  • TBC1 Domain Family, Member 20 2
  • WARBM4 3

External Ids for TBC1D20 Gene

Previous HGNC Symbols for TBC1D20 Gene

  • C20orf140

Previous GeneCards Identifiers for TBC1D20 Gene

  • GC20M000367

Summaries for TBC1D20 Gene

Entrez Gene Summary for TBC1D20 Gene

  • This gene encodes a protein that belongs to a family of GTPase activator proteins of Rab-like small GTPases. The encoded protein and its cognate GTPase, Rab1, bind the nonstructural protein 5A (NS5A) of the hepatitis C virus (HCV) to mediate viral replication. Depletion of this protein inhibits replication of the virus and HCV infection. Mutations in this gene are associated with Warburg micro syndrome 4. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

GeneCards Summary for TBC1D20 Gene

TBC1D20 (TBC1 Domain Family Member 20) is a Protein Coding gene. Diseases associated with TBC1D20 include Warburg Micro Syndrome 4 and Hepatitis C Virus. Among its related pathways are Transport to the Golgi and subsequent modification and Vesicle-mediated transport. GO annotations related to this gene include GTPase activator activity and Rab GTPase binding.

UniProtKB/Swiss-Prot for TBC1D20 Gene

  • GTPase-activating protein specific for Rab1 and Rab2 small GTPase families for which it can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TBC1D20 Gene

Genomics for TBC1D20 Gene

Regulatory Elements for TBC1D20 Gene

Enhancers for TBC1D20 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20F000359 1.5 Ensembl ENCODE 65.2 +98.7 98735 8.0 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YBX1 YY1 SLC30A9 ZNF143 ZNF263 TBC1D20 ACTG1P3 ENSG00000272874 DEFB129 DEFB126 DEFB125 CSNK2A1 RBCK1 ENSG00000206797 C20orf96
GH20F000368 1.8 FANTOM5 Ensembl ENCODE 25 +90.0 90033 8.0 ARNT CREB3L1 MLX ZFP64 ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF766 TBC1D20 TRIB3 ENSG00000272874 DEFB129 DEFB126 DEFB125 RBCK1 SRXN1 ENSG00000206797 CSNK2A1
GH20F001185 1.3 Ensembl ENCODE 33.3 -724.6 -724598 3.2 HDGF ARNT ARID4B DMAP1 YBX1 YY1 SLC30A9 ZNF143 ZNF207 ZNF263 TBC1D20 ACTG1P3 SDCBP2-AS1 ENSG00000229728 TMEM74B ENSG00000274269
GH20F000399 1.7 FANTOM5 Ensembl ENCODE 21.3 +60.9 60898 4.7 PKNOX1 ARNT CREB3L1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 TBC1D20 ACTG1P3 RBCK1 ENSG00000229728 SOX12 TRIB3 ZCCHC3 CSNK2A1 GC20P000382 GC20P000386
GH20F001415 1.7 FANTOM5 Ensembl ENCODE 21.2 -955.1 -955050 4.4 ARNT MLX ARID4B SIN3A DMAP1 ZNF143 FOS SP3 JUNB REST TBC1D20 ACTG1P3 SDCBP2 NSFL1C FKBP1A SIRPA LOC105372497 GC20M001435
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TBC1D20 on UCSC Golden Path with GeneCards custom track

Promoters for TBC1D20 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000007798 453 2201 PKNOX1 ATF1 ARNT CREB3L1 MLX ARID4B SIN3A ZNF48 ZNF2 YY1

Genomic Location for TBC1D20 Gene

Chromosome:
20
Start:
435,477 bp from pter
End:
462,553 bp from pter
Size:
27,077 bases
Orientation:
Minus strand

Genomic View for TBC1D20 Gene

Genes around TBC1D20 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TBC1D20 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TBC1D20 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TBC1D20 Gene

Proteins for TBC1D20 Gene

  • Protein details for TBC1D20 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96BZ9-TBC20_HUMAN
    Recommended name:
    TBC1 domain family member 20
    Protein Accession:
    Q96BZ9
    Secondary Accessions:
    • A8K6I3
    • B9A6M1
    • Q5JWQ7
    • Q6ZSY8
    • Q96NE1
    • Q9BYM7
    • Q9H140

    Protein attributes for TBC1D20 Gene

    Size:
    403 amino acids
    Molecular mass:
    45855 Da
    Quaternary structure:
    • Directly interacts with the N-terminal amphipathic helix of hepatitis C virus (HCV) NS5A.

    Three dimensional structures from OCA and Proteopedia for TBC1D20 Gene

    Alternative splice isoforms for TBC1D20 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TBC1D20 Gene

Post-translational modifications for TBC1D20 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TBC1D20 Gene

No data available for DME Specific Peptides for TBC1D20 Gene

Domains & Families for TBC1D20 Gene

Protein Domains for TBC1D20 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TBC1D20 Gene

Graphical View of Domain Structure for InterPro Entry

Q96BZ9

UniProtKB/Swiss-Prot:

TBC20_HUMAN :
  • The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rabs switch 2 glutamine and insert in Rabs active site.
Domain:
  • The arginine and glutamine fingers are critical for the GTPase-activating mechanism, they pull out Rabs switch 2 glutamine and insert in Rabs active site.
  • Contains 1 Rab-GAP TBC domain.
genes like me logo Genes that share domains with TBC1D20: view

No data available for Gene Families for TBC1D20 Gene

Function for TBC1D20 Gene

Molecular function for TBC1D20 Gene

UniProtKB/Swiss-Prot Function:
GTPase-activating protein specific for Rab1 and Rab2 small GTPase families for which it can accelerate the intrinsic GTP hydrolysis rate by more than five orders of magnitude.

Gene Ontology (GO) - Molecular Function for TBC1D20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005096 GTPase activator activity IEA,IDA 17684057
GO:0005515 protein binding IPI 17684057
GO:0017137 Rab GTPase binding IPI 17684057
genes like me logo Genes that share ontologies with TBC1D20: view
genes like me logo Genes that share phenotypes with TBC1D20: view

Human Phenotype Ontology for TBC1D20 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for TBC1D20 Gene

Localization for TBC1D20 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TBC1D20 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TBC1D20 gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
golgi apparatus 5
plasma membrane 3
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for TBC1D20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IDA 22491470
GO:0005789 endoplasmic reticulum membrane IDA 17684057
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030173 integral component of Golgi membrane IDA 17684057
genes like me logo Genes that share ontologies with TBC1D20: view

Pathways & Interactions for TBC1D20 Gene

genes like me logo Genes that share pathways with TBC1D20: view

Gene Ontology (GO) - Biological Process for TBC1D20 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001675 acrosome assembly IEA --
GO:0002088 lens development in camera-type eye IEA --
GO:0006888 ER to Golgi vesicle-mediated transport IMP 21680502
GO:0007030 Golgi organization IMP 17684057
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with TBC1D20: view

No data available for SIGNOR curated interactions for TBC1D20 Gene

Transcripts for TBC1D20 Gene

Unigene Clusters for TBC1D20 Gene

TBC1 domain family, member 20:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for TBC1D20 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11
SP1: - - - - -
SP2: - - -
SP3: - -
SP4: - - -
SP5: -
SP6:
SP7: - - -
SP8: -
SP9:
SP10:

Relevant External Links for TBC1D20 Gene

GeneLoc Exon Structure for
TBC1D20
ECgene alternative splicing isoforms for
TBC1D20

Expression for TBC1D20 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for TBC1D20 Gene

Protein differential expression in normal tissues from HIPED for TBC1D20 Gene

This gene is overexpressed in Bone (28.2) and Peripheral blood mononuclear cells (17.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TBC1D20 Gene



Protein tissue co-expression partners for TBC1D20 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TBC1D20 Gene:

TBC1D20

SOURCE GeneReport for Unigene cluster for TBC1D20 Gene:

Hs.590876
genes like me logo Genes that share expression patterns with TBC1D20: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for TBC1D20 Gene

Orthologs for TBC1D20 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for TBC1D20 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TBC1D20 34 35
  • 99.01 (n)
dog
(Canis familiaris)
Mammalia TBC1D20 34 35
  • 92.8 (n)
cow
(Bos Taurus)
Mammalia TBC1D20 34 35
  • 92.72 (n)
mouse
(Mus musculus)
Mammalia Tbc1d20 34 16 35
  • 89.3 (n)
rat
(Rattus norvegicus)
Mammalia Tbc1d20 34
  • 88.89 (n)
oppossum
(Monodelphis domestica)
Mammalia TBC1D20 35
  • 85 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 57 (a)
OneToMany
-- 35
  • 35 (a)
OneToMany
chicken
(Gallus gallus)
Aves TBC1D20 34 35
  • 80.38 (n)
lizard
(Anolis carolinensis)
Reptilia TBC1D20 35
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia tbc1d20.1 34
  • 73.89 (n)
Str.10618 34
African clawed frog
(Xenopus laevis)
Amphibia MGC52691 34
zebrafish
(Danio rerio)
Actinopterygii tbc1d20 34 35
  • 70.61 (n)
zgc63863 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008312 34
  • 54.2 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17883 34 35
  • 49.88 (n)
worm
(Caenorhabditis elegans)
Secernentea tbc-20 34 35
  • 49.6 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GYP8 35
  • 16 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 46 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU05272 34
  • 44.1 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes gyp10 34
  • 41.7 (n)
Species where no ortholog for TBC1D20 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TBC1D20 Gene

ENSEMBL:
Gene Tree for TBC1D20 (if available)
TreeFam:
Gene Tree for TBC1D20 (if available)

Paralogs for TBC1D20 Gene

No data available for Paralogs for TBC1D20 Gene

Variants for TBC1D20 Gene

Sequence variations from dbSNP and Humsavar for TBC1D20 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs587777157 Pathogenic 447,946(+) TTTTC(A/G)TCTGA intron-variant, nc-transcript-variant, reference, stop-gained
rs587777158 Pathogenic 445,095(+) CACTT(A/G)TTGGT nc-transcript-variant, reference, stop-gained
rs587777159 Pathogenic 442,028(+) CTCTC(-/TG)TTCCT nc-transcript-variant, reference, frameshift-variant
rs587777160 Pathogenic 440,344(+) CCAAA(C/T)CAGGT nc-transcript-variant, reference, stop-gained
rs141648576 Uncertain significance 438,655(+) GCAGC(C/T)GCTCC nc-transcript-variant, reference, synonymous-codon

Structural Variations from Database of Genomic Variants (DGV) for TBC1D20 Gene

Variant ID Type Subtype PubMed ID
nsv9774 CNV gain 18304495
nsv585171 CNV loss 21841781
nsv469833 CNV gain 16826518
nsv458842 CNV loss 19166990
nsv1109347 CNV deletion 24896259
nsv1066598 CNV gain 25217958
nsv1056266 CNV gain 25217958
esv3644956 CNV gain 21293372
esv3644953 CNV gain 21293372
esv3644952 CNV gain 21293372
esv3556706 CNV deletion 23714750
esv2677224 CNV deletion 23128226
esv2535181 CNV deletion 19546169
esv1050414 CNV deletion 17803354
dgv4221n100 CNV gain 25217958
dgv4219n100 CNV gain 25217958

Variation tolerance for TBC1D20 Gene

Residual Variation Intolerance Score: 23.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.38; 54.11% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TBC1D20 Gene

Human Gene Mutation Database (HGMD)
TBC1D20
SNPedia medical, phenotypic, and genealogical associations of SNPs for
TBC1D20

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TBC1D20 Gene

Disorders for TBC1D20 Gene

MalaCards: The human disease database

(4) MalaCards diseases for TBC1D20 Gene - From: OMIM, ClinVar, GeneTests, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
warburg micro syndrome 4
  • warbm4
hepatitis c virus
  • hepatitic c virus
warburg micro syndrome 1
  • warburg micro syndrome
spastic diplegia
  • cerebral spastic infantile paralysis
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

TBC20_HUMAN
  • Warburg micro syndrome 4 (WARBM4) [MIM:615663]: A form of Warburg micro syndrome, a rare syndrome characterized by microcephaly, microphthalmia, microcornia, congenital cataracts, optic atrophy, cortical dysplasia, in particular corpus callosum hypoplasia, severe mental retardation, spastic diplegia, and hypogonadism. {ECO:0000269 PubMed:24239381}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for TBC1D20

Genetic Association Database (GAD)
TBC1D20
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TBC1D20
genes like me logo Genes that share disorders with TBC1D20: view

No data available for Genatlas for TBC1D20 Gene

Publications for TBC1D20 Gene

  1. Loss-of-Function Mutations in TBC1D20 Cause Cataracts and Male Infertility in blind sterile Mice and Warburg Micro Syndrome in Humans. (PMID: 24239381) Liegel R.P. … Sidjanin D.J. (Am. J. Hum. Genet. 2013) 3 4 64
  2. Catalytic mechanism of a mammalian RabA^RabGAP complex in atomic detail. (PMID: 23236136) Gavriljuk K. … Gerwert K. (Proc. Natl. Acad. Sci. U.S.A. 2012) 3 4 64
  3. Identification and characterization of a novel Tre-2/Bub2/Cdc16 (TBC) protein that possesses Rab3A-GAP activity. (PMID: 19077034) Ishibashi K. … Fukuda M. (Genes Cells 2009) 3 4 64
  4. TBC1D20 is a Rab1 GTPase-activating protein that mediates hepatitis C virus replication. (PMID: 17901050) Sklan E.H. … Glenn J.S. (J. Biol. Chem. 2007) 2 3 64
  5. A Rab-GAP TBC domain protein binds hepatitis C virus NS5A and mediates viral replication. (PMID: 17686842) Sklan E.H. … Glenn J.S. (J. Virol. 2007) 3 4 64

Products for TBC1D20 Gene

Sources for TBC1D20 Gene

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